Contacts of the strand formed by residues 124 - 130 (chain T) in PDB entry 2P8Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 124 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21T ASN 3.2 7.2 + - - -
22T MET* 3.0 28.6 - - - +
23T SER 3.4 2.6 + - - -
122T THR* 4.1 3.8 - - - -
123T ASP* 1.3 78.3 - - - +
125T ALA* 1.3 62.2 + - - +
151T ILE* 3.5 6.1 - - - +
152T LYS 3.2 11.2 - - - -
342T LEU* 4.0 13.7 - - - -
343T PRO* 4.3 5.3 + - - +
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Residues in contact with ALA 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T MET* 4.6 0.2 - - - -
23T SER* 3.5 13.9 - - - +
25T ILE* 3.9 29.6 - - + -
119T LEU* 5.7 1.1 - - + -
122T THR* 5.9 0.2 - - - +
124T GLY* 1.3 74.0 - - - +
126T LEU* 1.3 59.9 + - - +
127T VAL* 3.7 4.7 + - + -
143T LEU* 6.3 0.2 - - + -
146T ALA* 5.1 0.7 - - + -
151T ILE* 3.8 14.4 - - + -
152T LYS 2.8 10.6 + - - +
153T PRO* 3.5 3.6 - - + +
154T VAL* 3.0 30.5 + - - +
342T LEU* 3.9 7.5 - - - +
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Residues in contact with LEU 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T MET* 3.8 22.3 - - + +
23T SER 2.9 9.9 + - - +
24T VAL* 3.3 25.9 - - + +
25T ILE 2.9 22.7 + - - -
35T LEU* 5.1 4.9 - - + -
39T LEU* 4.9 7.0 - - + -
125T ALA* 1.3 70.5 - - - +
127T VAL* 1.3 62.6 + - - +
128T VAL* 4.7 5.6 - - + -
154T VAL* 3.5 22.0 - - + +
156T VAL* 3.0 36.8 - - + -
334T LEU* 4.4 24.2 - - + -
337T MET* 4.1 3.4 - - + -
338T ILE* 5.1 6.3 - - + -
342T LEU* 5.4 0.7 - - + -
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Residues in contact with VAL 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25T ILE* 3.5 26.9 - - + +
125T ALA* 4.2 3.8 - - + +
126T LEU* 1.3 74.3 - - - +
128T VAL* 1.3 62.6 + - - +
129T VAL* 3.8 9.8 + - + -
139T THR* 4.1 23.6 - - + -
143T LEU* 4.3 23.1 - - + -
153T PRO* 4.0 22.9 - - + -
154T VAL 2.6 19.4 + - - +
155T VAL* 3.3 14.4 - - + +
156T VAL 2.9 26.2 + - - -
185T VAL* 5.8 1.6 - - + -
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Residues in contact with VAL 128 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24T VAL* 3.5 29.8 - - + -
25T ILE 2.8 14.9 + - - +
26T ALA* 3.6 20.5 - - + -
30T HIS* 3.5 38.3 + - + +
31T GLY 5.0 0.9 - - - -
32T LYS* 4.8 2.9 - - - -
35T LEU* 3.6 24.2 - - + -
126T LEU* 4.3 5.2 - - + +
127T VAL* 1.3 72.6 - - - +
129T VAL* 1.3 67.1 + - - +
139T THR* 4.2 8.5 - - - +
156T VAL* 3.6 5.6 - - + +
158T ASN* 3.6 18.4 - - + -
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Residues in contact with VAL 129 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T HIS* 4.3 2.9 - - - -
127T VAL* 4.3 12.1 - - + -
128T VAL* 1.3 82.2 - - - +
130T ASP* 1.3 61.5 + - - +
134T GLY 3.4 24.2 - - - +
135T VAL* 3.7 15.9 - - + +
139T THR* 4.6 5.4 - - + -
155T VAL* 4.2 19.5 - - + -
156T VAL 2.9 8.6 + - - +
157T ILE* 3.3 5.3 - - - -
158T ASN* 2.7 32.4 + - - -
181T THR* 3.2 30.7 - - + -
185T VAL* 4.3 9.6 - - + -
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Residues in contact with ASP 130 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T HIS* 3.5 34.9 + - + +
129T VAL* 1.3 79.2 - - - +
131T THR* 1.3 67.7 + - - +
132T ILE* 3.0 13.3 + - - +
133T GLU* 2.7 35.8 + - + +
134T GLY* 2.9 21.8 + - - +
157T ILE* 4.5 1.0 - - - +
158T ASN* 4.0 4.0 - - - +
159T LYS* 3.2 40.7 - - - +
162T ARG* 4.4 8.8 + - - -
181T THR* 4.5 2.1 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il